Articles publicats (Ciència Animal)
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- ItemOpen AccessImpact of carob (Ceratonia siliqua L.) pulp inclusion and warm season on gastrointestinal morphological parameters, immune-redox defences and coccidiosis in concentrate-fed light lambs(Elsevier, 2023-08-11) Pelegrin-Valls, Jonathan; Álvarez Rodríguez, Javier; Martín-Alonso, María José; Aquilué, Beatriz; Serrano, BeatrizThis study aimed to evaluate the effects of dietary carob (Ceratonia siliqua L.) pulp and warm season on gastrointestinal morphological parameters, immune-redox defences and coccidiosis in concentrate-fed light lambs. Weaned lambs were assigned to one of three concentrate-based diets: C0 (without carob pulp), C15 (150 g/kg of carob pulp) and C30 (300 g/kg of carob pulp) from 40 to 80 days of age in two consecutive cold and warm batches. Blood samples were collected at Day 80 to determine the metabolic status. Rectal faeces were sampled at Days 50, 65 and 80 to determine consistency and oocyst count per gram. Inclusion of carob pulp in lamb diets did not affect lamb growth but reduced coccidia oocyst excretion, improved faecal consistency and gastrointestinal morphological parameters, enhancing the ruminal thickness of the papilla living strata and reducing the darkness of the epithelium colour. Moreover, carob condensed tannins in the lambs' diet enhanced the expression of antioxidant SOD2 in rumen, while down-regulated NRF2, SOD1, CAT and PPARG in ileum. There was no interaction between the treatments and season in the evaluated variables. Lambs from the warm season exhibited reduced growth performance, altered ruminal epithelium, lower circulating iron levels, increased protein concentrations and higher coccidiosis susceptibility. In addition, regulatory immune and antioxidant mechanisms to counterbalance reactive oxygen species production in gastrointestinal tissues were evident. Dietary inclusion of carob pulp (150 and 300 g/kg) in lamb diets improved gastrointestinal health and homeostasis but did not ameliorate the deleterious effects of warm season.
- ItemOpen AccessUsing pre‑selected variants from large‑scale whole‑genome sequence data for single‑step genomic predictions in pigs(BMC, 2023-07-26) Jang, Sungbong; Ros Freixedes, Roger; Hickey , John M.; Chen, Ching-Yi; Holl, Justin; Herring, William O.; Misztal, Ignacy; Lourenco, DanielaBackground Whole-genome sequence (WGS) data harbor causative variants that may not be present in standard single nucleotide polymorphism (SNP) chip data. The objective of this study was to investigate the impact of using preselected variants from WGS for single-step genomic predictions in maternal and terminal pig lines with up to 1.8k sequenced and 104k sequence imputed animals per line. Methods Two maternal and four terminal lines were investigated for eight and seven traits, respectively. The number of sequenced animals ranged from 1365 to 1491 for the maternal lines and 381 to 1865 for the terminal lines. Imputation to sequence occurred within each line for 66k to 76k animals for the maternal lines and 29k to 104k animals for the terminal lines. Two preselected SNP sets were generated based on a genome-wide association study (GWAS). Top40k included the SNPs with the lowest p-value in each of the 40k genomic windows, and ChipPlusSign included significant variants integrated into the porcine SNP chip used for routine genotyping. We compared the performance of single-step genomic predictions between using preselected SNP sets assuming equal or different variances and the standard porcine SNP chip. Results In the maternal lines, ChipPlusSign and Top40k showed an average increase in accuracy of 0.6 and 4.9%, respectively, compared to the regular porcine SNP chip. The greatest increase was obtained with Top40k, particularly for fertility traits, for which the initial accuracy based on the standard SNP chip was low. However, in the terminal lines, Top40k resulted in an average loss of accuracy of 1%. ChipPlusSign provided a positive, although small, gain in accuracy (0.9%). Assigning different variances for the SNPs slightly improved accuracies when using variances obtained from BayesR. However, increases were inconsistent across the lines and traits. Conclusions The benefit of using sequence data depends on the line, the size of the genotyped population, and how the WGS variants are preselected. When WGS data are available on hundreds of thousands of animals, using sequence data presents an advantage but this remains limited in pigs.
- ItemOpen AccessUsing residual regressions to quantify and map signal leakage in genomic prediction(BMC, 2023-08-07) Valente, Bruno D.; Campos, Gustavo de los; Grueneberg, Alexander; Chen, Ching-Yi; Ros Freixedes, Roger; Herring, William O.Background Most genomic prediction applications in animal breeding use genotypes with tens of thousands of single nucleotide polymorphisms (SNPs). However, modern sequencing technologies and imputation algorithms can generate ultra-high-density genotypes (including millions of SNPs) at an affordable cost. Empirical studies have not produced clear evidence that using ultra-high-density genotypes can significantly improve prediction accuracy. However, (whole-genome) prediction accuracy is not very informative about the ability of a model to capture the genetic signals from specific genomic regions. To address this problem, we propose a simple methodology that detects chromosome regions for which a specific model (e.g., single-step genomic best linear unbiased prediction (ssGBLUP)) may fail to fully capture the genetic signal present in such segments a phenomenon that we refer to as signal leakage. We propose to detect regions with evidence of signal leakage by testing the association of residuals from a pedigree or a genomic model with SNP genotypes. We discuss how this approach can be used to map regions with signals that are poorly captured by a model and to identify strategies to fix those problems (e.g., using a different prior or increasing marker density). Finally, we explored the proposed approach to scan for signal leakage of different models (pedigree-based, ssGBLUP, and various Bayesian models) applied to growth-related phenotypes (average daily gain and backfat thickness) in pigs. Results We report widespread evidence of signal leakage for pedigree-based models. Including a percentage of animals with SNP data in ssGBLUP reduced the extent of signal leakage. However, local peaks of missed signals remained in some regions, even when all animals were genotyped. Using variable selection priors solves leakage points that are caused by excessive shrinkage of marker effects. Nevertheless, these models still miss signals in some regions due to low linkage disequilibrium between the SNPs on the array used and causal variants. Thus, we discuss how such problems could be addressed by adding sequence SNPs from those regions to the prediction model. Conclusions Residual single-marker regression analysis is a simple approach that can be used to detect regional genomic signals that are poorly captured by a model and to indicate ways to fix such problems.
- ItemOpen AccessColour Stability, Fatty Acid Profile, and Lipid Oxidation in Meat Stored in Modified Atmosphere Packaging from Light Lambs Fed with Concentrate with Carob Pulp (Ceratonia siliqua L.)(MDPI, 2023-07-25) Bottegal, Diego Nicolas; Lobón, Sandra; Latorre, Maria Angeles; Bertolín, Juan Ramon; Álvarez Rodríguez, JavierThere is a growing interest in using by-products rich in polyphenols, such as carob pulp (Cp, Ceratonia siliqua L.), as a dietary source of antioxidants for animals. This study assesses the effects of including Cp in lambs' diet and meat display time (0, 7, 9, and 11 days) in modified atmosphere packaging on meat colour, fatty acid (FA) composition, tocopherol levels, and lipid oxidation values in the Semimembranosus muscle of 40 light lambs. The lambs were fed with concentrates supplemented with increasing Cp levels (0, 150, and 300 g/kg) for 45 days before slaughter. Metmyoglobin (MMb) and malondialdehyde (MDA) contents increased linearly with display time (p < 0.05), regardless of diet (p > 0.05). At 11 days of display, MMb (28 ± 0.8%) and MDA (0.6 ± 0.1 mg MDA/kg of meat) contents remained within the acceptable limits. The α-tocopherol content was lower in the 30% Cp group and meat (p < 0.05). Total saturated and monounsaturated FA contents (934 ± 64 and 823 ± 65 mg/100 g of meat, respectively) did not differ significantly among the groups. However, the meat from lambs fed with 30% Cp showed reduced levels of branched-chain FAs, while polyunsaturated FAs increased (p < 0.05) compared to the control lambs. The inclusion of Cp in the lamb's diet, up to 30%, did not lead to meat deterioration and improved certain quality parameters, including a healthier FA profile. These findings highlight Cp's potential as an alternative antioxidant source in animal diets.
- ItemOpen AccessCorrection to: Diseases of Iberian ibex (Capra pyrenaica) (European Journal of Wildlife Research, (2023), 69, 3, (63), 10.1007/s10344-023-01684-0)(Springer Science and Business Media Deutschland GmbH, 2023-08) Valldeperes, Marta; Yerro, Paloma Prieto; López-Olvera, Jorge Ramón; Fandos, Paulino; Lavín, Santiago; Escofet, Ramón C. Soriguer; Mentaberre García, Gregorio; León, Francisco Javier Cano‑Manuel; Espinosa, José; Raez‑Bravo, Arián; Pérez, Jesús M.; Tampach, Stefania; Estruch, Josep
